BamQC report ----------------------------------- >>>>>>> Input bam file = SRR927028.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 28,378,786 number of mapped reads = 27,962,928 (98.53%) number of supplementary alignments = 229,668 (0.81%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 14,022,121 number of mapped paired reads (second in pair) = 13,940,807 number of mapped paired reads (both in pair) = 27,719,268 number of mapped paired reads (singletons) = 243,660 number of mapped bases = 2,649,380,742 bp number of sequenced bases = 2,647,396,733 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,846,288 duplication rate = 4.95% >>>>>>> Insert size mean insert size = 87,058.9986 std insert size = 2,883,633.0518 median insert size = 202 >>>>>>> Mapping quality mean mapping quality = 53.5463 >>>>>>> ACTG content number of A's = 767,185,550 bp (28.98%) number of C's = 521,751,080 bp (19.71%) number of T's = 775,431,457 bp (29.29%) number of G's = 582,449,607 bp (22%) number of N's = 579,039 bp (0.02%) GC percentage = 41.71% >>>>>>> Mismatches and indels general error rate = 0.0095 number of mismatches = 24,350,650 number of insertions = 426,431 mapped reads with insertion percentage = 1.5% number of deletions = 1,406,190 mapped reads with deletion percentage = 4.9% homopolymer indels = 53.16% >>>>>>> Coverage mean coverageData = 0.8558X std coverageData = 4.0371X There is a 34.18% of reference with a coverageData >= 1X There is a 19.1% of reference with a coverageData >= 2X There is a 11.12% of reference with a coverageData >= 3X There is a 6.81% of reference with a coverageData >= 4X There is a 4.3% of reference with a coverageData >= 5X There is a 2.77% of reference with a coverageData >= 6X There is a 1.82% of reference with a coverageData >= 7X There is a 1.21% of reference with a coverageData >= 8X There is a 0.82% of reference with a coverageData >= 9X There is a 0.56% of reference with a coverageData >= 10X There is a 0.39% of reference with a coverageData >= 11X There is a 0.27% of reference with a coverageData >= 12X There is a 0.19% of reference with a coverageData >= 13X There is a 0.14% of reference with a coverageData >= 14X There is a 0.1% of reference with a coverageData >= 15X There is a 0.07% of reference with a coverageData >= 16X There is a 0.06% of reference with a coverageData >= 17X There is a 0.04% of reference with a coverageData >= 18X There is a 0.04% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 208326481 0.8358112816898459 5.648628003159321 chr2 243199373 233897435 0.9617518010624148 5.99000769882632 chr3 198022430 184395809 0.9311864772086678 1.8474788690241168 chr4 191154276 165984702 0.8683284803945479 2.6058804325106526 chr5 180915260 165280835 0.9135815021905835 1.771732805064645 chr6 171115067 152560530 0.891566901002353 1.7992678142108263 chr7 159138663 138917180 0.8729316772002791 2.4940468509139753 chr8 146364022 138310071 0.944973150573848 2.142545963562061 chr9 141213431 106781309 0.7561696379999435 4.52674259877697 chr10 135534747 136139300 1.0044605019257533 10.654094639295453 chr11 135006516 125434961 0.9291030145537568 4.224298753343086 chr12 133851895 121383051 0.9068459658341035 1.783882004186222 chr13 115169878 83028091 0.7209184592519929 1.5587005970756551 chr14 107349540 78498426 0.7312413821242271 1.645770528980516 chr15 102531392 78424011 0.7648780482761807 1.67294810395459 chr16 90354753 80310721 0.888837812439153 5.090908431234918 chr17 81195210 65706354 0.8092392888693803 2.2583618126644502 chr18 78077248 68770938 0.8808063778067587 4.954604333630997 chr19 59128983 39165470 0.662373475965247 3.115787894759753 chr20 63025520 58783196 0.9326887901916557 1.9835507384576547 chr21 48129895 32161238 0.6682174976695877 2.3455365899706644 chr22 51304566 30010193 0.5849419523400705 1.542611920372375 chrMT 16571 135843 8.197634421579869 6.579483533962462 chrX 155270560 152523096 0.9823053127392598 2.240754471001337 chrY 59373566 4451501 0.07497445917262238 2.3286677687771107